DBBS Cerebellar models

This repository provides the code, configuration and morphology data to reconstruct and simulate cerebellar circuits using the Brain Scaffold Builder. These models are based on the iterative work of the Department of Brain and Behavioral Sciences of the University of Pavia.

Getting Started

• Installation
  • NEST simulator
  • What next:
• Biological context
• Contents
  • Morphologies
  • BSB configuration files for the cerebellar cortex
• Building a first circuit
  • Introduction to BSB
  • A modular configuration file to reconstruct cerebellar cortex circuit
  • Reconstruction of the rodent canonical circuit
  • Simulation of the reconstructed circuits
• Customising configurations with BSB imports
  • How $import works
  • Pattern 1 — importing top-level sections
  • Pattern 2 — importing a subsection into a nested context
  • Pattern 3 — overriding imported values
  • Creating a custom simulation
  • Further reading
• For developers
  • Documentation
  • Testing
  • Configuration file layout

CLI

• Command-Line Interface
  • Retrieve a canonical circuit configuration
  • Re-compile NESTML neuron models

BSB Configurations

• Circuit configurations
  • Mouse
    • Mouse cerebellar cortex configuration
    • Extra Cell types for the canonical model
    • NEST simulations
    • Neuron simulations
• Neuron Morphologies configurations

Strategies

• Placement strategies
  • LabelCells
  • LabelMicrozones
• Connection strategies
  • ConnectomeMossyGlomerulus
  • ConnectomeGlomerulusGolgi
  • ConnectomeGlomerulusGranule
  • ConnectomeGolgiGlomerulus
  • VoxelIntersection
  • ConnectomeUBCGlomerulus
  • ConnectomeGlomerulusUBC
  • ConnectomeIO_MLI
  • FixedIndegree
  • AllToAll
  • DuplicateSynapses

Analysis and Reporting

• Analysis and reporting
  • Introduction to plotting
  • Structural analysis and report
  • Spike results extraction and analysis
  • Plots and reports of spiking results

Code references

• Packages
  • cerebellar_models package
• Index
• Module Index